OSLay: optimal syntenic layout of unfinished assemblies | Zendy

Daniel C. Richter | Zendy; Stephan C. Schuster | Zendy; Daniel H. Huson | Zendy

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OSLay: optimal syntenic layout of unfinished assemblies

Author(s) -

Daniel C. Richter,

Stephan C. Schuster,

Daniel H. Huson

Publication year - 2007

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btm153

Subject(s) - contig , sequence assembly , synteny , computer science , genome , software , shotgun sequencing , closure (psychology) , visualization , computational biology , data mining , biology , genetics , programming language , gene expression , gene , economics , market economy , transcriptome

The whole genome shotgun approach to genome sequencing results in a collection of contigs that must be ordered and oriented to facilitate efficient gap closure. We present a new tool OSLay that uses synteny between matching sequences in a target assembly and a reference assembly to layout the contigs (or scaffolds) in the target assembly. The underlying algorithm is based on maximum weight matching. The tool provides an interactive visualization of the computed layout and the result can be imported into the assembly editing tool Consed to support the design of primer pairs for gap closure.

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